From the outside inward: the first and second circles show predicted protein-coding regions on the plus and minus strands, by biological role: translation/ribosome structure/biogenesis, pink; transcription, olive drab; DNA replication/recombination/repair, forest green; cell division/chromosome partitioning, light blue; posttranslational modification/protein turnover/chaperones, purple; cell envelop biogenesis, red; cell motility/secretion, plum; inorganic ion transport/metabolism, dark sea green; signal transduction mechanisms, medium purple; energy production/conversion, dark olive green; carbohydrate transport/metabolisms, gold; amino acid transport/metabolism, yellow; nucleotide transport/metabolism, orange; coenzyme transport/metabolism, tan; lipid transport/metabolism, salmon; secondary metabolites biosynthesis/transport/catabolism, light green; defense mechanism, black; general function prediction only, dark blue; function unknown and hypothetical protein, gray. The third circle shows G+C content percentage in relation to the mean G+C% for the chromosome. The fourth circle shows GC skew. The fifth circle shows insertion sequences, retrotransposons (black) and prophage (orange). The sixth and seventh circles show tRNA genes and rRNA operons, with blue or black on the plus strand and red on the minus one.

The phylogenetic tree of the 16S rRNA gene sequences from various Shewnaella species was constructed by neighbor-joining method using the programs of MEGA package. 1000 trial of bootstrap analysis was used to provide confident estimates for phylogenetic tree topologies. The phylogenetic tree based on the whole proteome sequences of the strains was constructed as described in the materials and methods with 100 trial of bootstrap.

The function classification of shared genes in 13 compared Shewanella genomes was based on Gene Ontology term. Of all common genes, those belong to nucleic acid binding, nucleotide binding, hydrolase activity, transferase activity and oxidoreductase activity are predominant.

The mtr-omc gene clusters in several Shewanella genomes are illustrated. The conserved mtrBAC operon is boxed. hypP represents gene for hypothetical protein, spoP encodes for phage SPO1 DNA polymerase domain protein. 1, Shewanella sp. MR4; S. sp.ANA3; S. sp. MR7; S. baltica OS155; 2, S. oneidensis MR-1; S. baltica OS185; 3, S.frigidimarina NCIMB400; 4, S.putrefaciens CN32; 5, S. sp. W3-18-1; 6, S. amazonensis SB2B; 7, S. Loihica PV4; 8, S.piezotolerans WP3.

The growth of WP3 and the WP3Δorf2 mutant under different temperature and pressure conditions were monitered by measuring the optical density of the cultutes at 0D₆₀₀. For each measurement, triplicate cultures were measured simultaneously, and the average value was recorded. A: Growth of the strains at 0.1 MPa and 20 MPa. Wild type WP3 was grown at 0.1 MPa (□), or at 20 MPa (▪); WP3Δorf2 mutant grown at 0.1 MPa (▴) or 20 MPa(Δ); B: Growth of the strains at 4°C and 20°C. Wild type WP3 was grown at 4°C (□), or at 20°C (▪); WP3Δorf2 mutant grown at 4°C (▴) or 20°C (Δ).

A: Flagellum gene cluster I (polar): swp1493—swp1550; B: Flagellum gene cluster II (lateral): swp5082—swp5126. Arrow indicates gene transcription direction.

The WP3 cells from liquid culture and from agar plates were visualized by TEM separately. The cells from liquid culture were shown to have polar flagellum (A); while the cells from ager plates also contain lateral flagellum (B). The transcription level of four genes (swp1499, swp1511, swp1508, swp1519) for polar flagellum synthesis and four genes (swp5109, swp5114, swp5118, swp5125) for lateral flagellum synthesis under different temperatures and pressures were checked by Quantitative RT-PCR as described in the materials and methods. C: The transcription changes of genes at 20 MPa as compared with that at 0.1 MPa. The transcription levels of the genes at 0.1 MPa are set as control; D: The transcription change of genes at 4°C as compared with that at 20°C. The transcription levels of the genes at 20°C are set as control

The motility assays for WP3 and the mutants (WP3Δ1508 has defect in polar flagellum; WP3Δ5118, WP3Δ5125 defect in lateral flagellum) were conducted on 0.3% agar plates at 20°C (A) or 4°C (B). Triplicates of each strain were spotted onto the soft agar, the motile ability of the strains were compared by observing the movements of the strains after 3 days at 20°C, or 7 days at 4°C. The growth of WP3 and the mutants at 4°C was monitered by measuring the optical density of the cultutes at 0D₆₀₀. The mean values with standard deviations (indicated by vertical bars) from triplicate experiments are given. Δ represents the wild type WP3; • mutant WP3Δ1508; ○WP3Δ5118 ▾WP3Δ5125.